Please install the latest versions of
,
RStudio, and git.
Having an up-to-date environment is the first good practice.
Click on Download R for Windows
Click on base
Click on Download R 4.1.2 for Windows
Open R-4.1.2-win.exe and follow instructions
RStudio Desktop at:
Download the version for Windows 10 (the .exe and not
the .zip)
Open RStudio-2021.09.0-351.exe and follow instructions
Check if RStudio has found
.
Launch RStudio and run:
R.version.string
## [1] "R version 4.1.2 (2021-11-01)"
git at:
Download the 64-bit version for Windows
Open Git-2.33.1-64-bit.exe and follow instructions
Check if RStudio has found
git. Launch
RStudio and run:
Sys.which("git")
## C:/Program Files/Git/bin/git.exe
Rtools4 at:
Download the 64-bit version for Windows
Open rtools40v2-x86_64.exe and follow instructions
The installation of Rtools4 is
optional, but this software is required to install packages (from
sources) containing compiled code (C/C++/Fortran).
Rtools4 contains in particular the utility
make.
Once Rtools4 is installed, you need to
tell
where to find Rtools4 utilities. Open
RStudio et run:
cat("PATH='${RTOOLS40_HOME}\\usr\\bin;${PATH}'\r\n", file = "~/.Renviron", append = TRUE)
An hidden file .Renviron has been created (or modified)
in you personal folder and contains the line
PATH='${RTOOLS40_HOME}\\usr\\bin;${PATH}' (the path to
Rtools4). At each start
will read this file.
Restart RStudio and check that
find make:
Sys.which("make")
## "C:/rtools40/usr/bin/make.exe"
Now you can install packages from sources:
install.packages("jsonlite", type = "source")
pandocThe package rmarkdown requires the
software pandoc to convert document from
one format (e.g. .Rmd) to another
(e.g. .html).
Download pandoc at: https://github.com/jgm/pandoc/releases/tag/2.16.1,
and follow instructions.
LaTeX distributionIf you want to convert documents from .Rmd to
.pdf, you will need LaTeX.
You can install a lightened distribution using the
package tinytex.
Open RStudio and run:
## Install tinytex ----
install.packages("tinytex")
## Install LaTeX ----
tinytex::install_tinytex()
N.B. If you already have a
LaTeX distribution, do not install
tinytex.
Th easiest way to set up your environment is by using the package
manager for macOS Homebrew. With
this tool you can install (and update) your software directly from the
terminal. First you need to install the Apple software Command Line
Tools for Xcode.
Open a terminal, run this line and accept the license:
## Install Xcode Command Line Tools ----
sudo xcode-select --installThen you can install Homebrew:
## Install Homebrew ----
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
## Check installation ----
brew --version
## Homebrew 3.3.8
## Update repositories (list of available software) ----
brew updateFollow these lines to install your environment:
## Install utilities for R ----
brew install --cask xquartz ## Graphical window system
brew install gfortran ## FORTRAN compiler for GCC
## Install R ----
brew install --cask r
## Install RStudio Desktop ----
brew install --cask rstudio
## Install git ----
brew install git
## Install pandoc ----
brew install pandoc ## Convert documents (Rmd, html, etc.)Open RStudio and check your
installation:
If you want to convert documents from .Rmd to
.pdf, you will need LaTeX.
You can install a lightened distribution using the
package tinytex.
Open RStudio and run:
## Install tinytex ----
install.packages("tinytex")
## Install LaTeX ----
tinytex::install_tinytex()
Congrats! You have successfully install your environment. The
following commands will install system libraries (software) required by
some
packages (sf, sp, rgdal,
rgeos, raster, terra,
xml, etc.).
## Install other utilities for R (spatial and others) ----
brew install libgit2
brew install libxml2
brew install poppler
brew install geos gdal netcdf proj udunitsTo keep your system up-to-date run frequently:
## Update environment ----
brew update && brew upgrade --greedyTo keep your system up-to-date, do not forget to frequently run:
## System update ----
sudo apt update && sudo apt upgradeThen check your version of Ubuntu:
## Check Ubuntu version ----
cat /etc/issue
## Ubuntu 20.04 LTS| Release | Release name | Repository URL |
|---|---|---|
| 21.04 | Hirsute Hippo | https://cloud.r-project.org/bin/linux/ubuntu hirsute-cran40/ |
| 20.10 | Groovy Gorilla | https://cloud.r-project.org/bin/linux/ubuntu groovy-cran40/ |
| 20.04 LTS | Focal Fossa | https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/ |
| 18.04 LTS | Bionic Beaver | https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/ |
| 16.04 LTS | Xenial Xerus | https://cloud.r-project.org/bin/linux/ubuntu xenial-cran40/ |
Install by following these steps (change the URL below by the one specific to your version of Ubuntu, cf. Table 1) :
## Install APT utilities ----
sudo apt install software-properties-common
## Add CRAN GPG key ----
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
## Add CRAN repository to APT repositories list ----
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
## Update packages list ----
sudo apt update
## Install R ----
sudo apt install r-base
## Install R (for development, recommended) ----
sudo apt install build-essential
sudo apt install r-base-devTo install RStudio Desktop visit this
page: https://www.rstudio.com/products/rstudio/download/#download,
download the .deb file for Ubuntu 18/Debian 10 et install
it. If you have an older version of Ubuntu (16.04), visit this page: https://www.rstudio.com/products/rstudio/older-versions/
Alternatively, you can install
RStudio Desktop from the terminal:
## Install wget utility ----
sudo apt install wget
## Download RStudio Desktop installer (Ubuntu >= 18.04) ----
wget https://download1.rstudio.org/desktop/bionic/amd64/rstudio-2021.09.0-351-amd64.deb
## Download RStudio Desktop installer (Ubuntu 16.04 only) ----
# wget https://download1.rstudio.org/desktop/xenial/amd64/rstudio-1.4.1106-amd64.deb
## Install RStudio Desktop ----
sudo dpkg -i rstudio-2021.09.0-351-amd64.deb
# sudo dpkg -i rstudio-1.4.1106-amd64.deb
## Remove installer ----
rm rstudio-2021.09.0-351-amd64.deb
# rm rstudio-1.4.1106-amd64.debNow let’s install git:
sudo apt install gitFinally, install pandoc (to convert
documents using rmarkdown):
sudo apt install pandocOpen RStudio and check your
installation:
If you want to convert documents from .Rmd to
.pdf, you will need LaTeX.
You can install a lightened distribution using the
package tinytex.
Open RStudio and run:
## Install tinytex ----
install.packages("tinytex")
## Install LaTeX ----
tinytex::install_tinytex()
Congrats! You have successfully install your environment. The
following commands will install system libraries (software) required by
some
packages (sf, sp, rgdal,
rgeos, raster, terra,
xml, etc.).
## Install other utilities for R (spatial and others) ----
sudo apt install libgdal-dev libproj-dev libgeos-dev libudunits2-dev libnetcdf-dev
sudo apt install libcairo2-dev libmagick++-dev
sudo apt install libpoppler-cpp-devTo keep your system up-to-date, do not forget to frequently run:
## Update system ----
sudo apt update && sudo apt upgradegitTo use git, you need to store your
credentials (user name and email) that will be added to all your
commits. Open a terminal (you can use the terminal of
RStudio) and run:
git config --global user.name "Jane Doe"
git config --global user.email "jane.doe@mail.com"When you create a new git project the default branch will be named master. It’s recommended to replace master by main (for more information read this article).
On a terminal, run:
git config --global init.defaultBranch "main"From now when you will initialize git in a new project
the default branch will be main.
To communicate with GitHub, you can use the protocol HTTPS (default) or the protocol SSH (recommended). The protocol SSH is a more secure method of logging into a remote server (GitHub). To use this protocol, you need to generate an SSH keys pair that consists in creating two long strings of characters: a public key and a private key. You can place the public key on any server (for instance GitHub), and then connect to the server using a device (your laptop) that has access to the private key.
To generate a new SSH keys pair proceed as follow:
Create an account on GitHub at https://github.com/signup
Open RStudio and click on:
Tools > Global options > Git/SVN
Click on Create RSA Key and then click on
Create (you can omit the passphrase). This new SSH keys
pair has been stored in ~/.ssh/.
Click on View public key and copy it
Go to the page https://github.com/settings/keys
and click on New SSH key
Choose a name for your key (e.g. your laptop name) and paste your
public key.
Finally click on Add SSH key
If you are on Ubuntu you need to install the following utility:
sudo apt install ssh-askpassLet’s test the SSH connection with GitHub. Open a terminal and run
(you need to accept the fingerprint, just enter yes):
ssh -T git@github.comCongrats! You can now communicate with GitHub using the SSH protocol.
From now, you need to use the SSH URL when connecting a new GitHub
project (named remote).
## URL HTTPS ----
https://github.com/frbcesab/datatoolbox.git
## URL SSH (use this one) ----
git@github.com:frbcesab/datatoolbox.gitIf you lose your private SSH key you won’t be able to establish a connection with GitHub. You’ll need to delete your SSH key on GitHub and to create a new one.
If you want to use the GitHub API, essentially with the
package usethis,
you need to create a GitHub Personal Access Token (PAT).
Go to https://github.com/settings/tokens
Click on Generate new token
Choose a name for your new token (e.g. your laptop name)
In the section scopes, select at least repo
and workflow
Copy this token.
Then open RStudio and run:
## Install usethis package ----
install.packages("usethis")
## Open ~/.Renviron file ----
usethis::edit_r_environ()
## • Modify '~/.Renviron'
## • Restart R for changes to take effect
In the ~/.Renviron file, add this new line:
GITHUB_PAT='XXX' where XXX is your token. Do
not forget to restart
.
Finally let’s tell usethis to use the SSH protocol. Open
RStudio and run:
## Install usethis package ----
install.packages("usethis")
## Open ~/.Rprofile file ----
usethis::edit_r_profile()
## • Modify '~/.Rprofile'
## • Restart R for changes to take effect
In the ~/.Rprofile file, add this new line:
options(usethis.protocol = "ssh"). Do not forget to restart
.
If you see mistakes or want to suggest changes, please Create an issue on the source repository.
The material of this website is licensed under Creative Commons Attribution CC BY 4.0. Source code is available at https://github.com/rdatatoolbox/rdatatoolbox.github.io/.
Casajus N, Dray S, Gimenez O, Guéry L, Guilhaumon F & Schiettekatte NMD (2021) Workshop FRB-CESAB & GdR EcoStat: Data Toolbox for Reproducible Research in Ecology (Edition 2021). Zenodo. http://doi.org/10.5281/zenodo.4262978.